Have you given thought to adding a '#theme' attribute to the form in hook_form_alter E.g. $form['#theme'] = 'my_theme_function'
Then either use your template (defined in hook_theme for the my_theme_function) or make the function stitch the fields together in the required format See http://drupal.org/node/751826 under 'Theming forms' for examples/details etc >But, what gets used/displayed by my user-login.tpl.php continues to use the 'standard' authenticator, NOT my custom one.
